FEMS microbiology ecology最新文献_第6页

Three novel Rothia species associated with Antarctic birds harbour novel biosynthetic gene clusters. 三种与南极鸟类相关的新罗氏属含有新的生物合成基因簇。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-06-18 DOI: 10.1093/femsec/fiag056

Vendula Koublová, Jana Musilova, Karel Sedlar, Peter Spacek, Jitka Vives, Eva Staňková, Ondrej Šedo, Stanislava Kralova, Ludek Sehnal, Ivo Sedláček, Pavel Švec

{"title":"Three novel Rothia species associated with Antarctic birds harbour novel biosynthetic gene clusters.","authors":"Vendula Koublová, Jana Musilova, Karel Sedlar, Peter Spacek, Jitka Vives, Eva Staňková, Ondrej Šedo, Stanislava Kralova, Ludek Sehnal, Ivo Sedláček, Pavel Švec","doi":"10.1093/femsec/fiag056","DOIUrl":"10.1093/femsec/fiag056","url":null,"abstract":"Antarctica's unique environment supports diverse avian populations, including penguins, skuas, and gulls. As climate-driven pressures on these populations intensify, their microbiota receives increased attention due to their relevance for host health. In this study, we investigated 11 bacterial isolates associated with Antarctic birds using a polyphasic taxonomic approach integrating genomic and phenotypic data. Phylogenetic analysis of 16S rRNA gene sequences and core-genome-based phylogenomics separated the strains into three groups and genome-relatedness indices confirmed that the three lineages represent novel species within the genus Rothia. Functional genomic analysis, combined with phenotypic testing, revealed broad metabolic capabilities with adaptations to host-associated environment. Further genome mining revealed the presence of several biosynthetic gene clusters, potentially encoding terpenes, siderophores, and other bioactive compounds. Some of these clusters likely encode variants of enterobactin, a nonribosomally synthesized siderophore. However, in vitro production of enterobactin was not confirmed, suggesting more complex expression regulation than iron depletion alone. Together, these findings broaden the known diversity of Rothia by three proposed novel species, Rothia ornithocola sp. nov., Rothia pygoscelis sp. nov., and Rothia antarctica sp. nov., and highlight genomic and phenotypic features that contribute to the ecology of Antarctic avian-associated bacteria.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13347742/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148053682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces. 土壤微生物生态学和微生物组-代谢物的联系提高了对陆水界面生态系统状态的理解。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-06-18 DOI: 10.1093/femsec/fiag066

Sreejata Bandopadhyay, Robert E Danczak, Kaizad F Patel, Kathleen R Beilsmith, Pamela B Weisenhorn, Trisha L Spanbauer, Nicholas J Reichart, Michael N Weintraub, Vanessa L Bailey

{"title":"Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces.","authors":"Sreejata Bandopadhyay, Robert E Danczak, Kaizad F Patel, Kathleen R Beilsmith, Pamela B Weisenhorn, Trisha L Spanbauer, Nicholas J Reichart, Michael N Weintraub, Vanessa L Bailey","doi":"10.1093/femsec/fiag066","DOIUrl":"10.1093/femsec/fiag066","url":null,"abstract":"Coastal soils are dynamic systems where unique microbial niches are shaped by the intensity and duration of flooding between the terrestrial and aquatic boundaries of the terrestrial-aquatic interface (TAI). We aimed to understand the soil microbial community (16S rRNA gene) along the TAIs of a freshwater versus estuarine region and how it relates to organic matter (OM, via Fourier Transform Ion Cyclotron Resonance Mass Spectrometry). We studied the TAI gradients along a transect from upland (forested), transition (stressed forest), to wetland at three sites in each of the Lake Erie (freshwater) and Chesapeake Bay (estuarine) regions. Microbial communities differed significantly by region, transect position, and site. Contrary to expectations, given their dynamic hydrologies, transitions represented midpoints in microbial richness and diversity. We identified a core microbiome conserved across all transect positions within a region, highlighting potential microbial functions most resilient to environmental change. Indicator taxa unique to each transect position defined specific niches shaped by soil biogeochemistry. Co-expression networks of feature-level β-nearest-taxon indices revealed positive relationships in bacterial and OM feature contributions to community assembly. Our study provides critical insights into microbial communities at the forefront of hydrological changes in coastal areas that connect the land to lakes and oceans and remain vulnerable to changing weather patterns.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13348248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148307571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Desiccation, but not shading, substantially shifts the microbial community composition of benthic microbial mats in meltwater ponds near Bratina Island, Antarctica. 干燥，而不是遮荫，实质上改变了南极Bratina岛附近融水池塘底栖微生物席的微生物群落组成。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-06-18 DOI: 10.1093/femsec/fiag069

Stephen E Noell, Elizabeth C Colville, Alexis Marshall, Ian Hawes, Ian R McDonald

{"title":"Desiccation, but not shading, substantially shifts the microbial community composition of benthic microbial mats in meltwater ponds near Bratina Island, Antarctica.","authors":"Stephen E Noell, Elizabeth C Colville, Alexis Marshall, Ian Hawes, Ian R McDonald","doi":"10.1093/femsec/fiag069","DOIUrl":"10.1093/femsec/fiag069","url":null,"abstract":"The Bratina Island meltwater ponds (McMurdo Ice Shelf, Antarctica) host complex microbial communities in the form of benthic microbial mats. These ponds are long-lasting but can experience significant alterations in physicochemistry on an annual or decadal basis, with additional alterations expected due to climate change. Here, we explored the impact of two potential future climate scenarios on the 16S rRNA gene sequence-based microbial community composition of three meltwater pond mats: desiccation (due to decreased precipitation and/or increased evaporation) and shading (due to increased precipitation resulting in increased ice cover). In a multi-year manipulation experiment, we found that the mat bacterial community composition shifted substantially with desiccation in all ponds studied. Desiccation reduced overall diversity, with cyanobacteria mostly being lost and members of the Bacteroidota phylum increasing in relative abundance. Halotolerance was indicated as a potential trait allowing for survival upon desiccation. We found that the community composition of the mats was resilient to shading (in the form of 75% light reduction), with no significant changes in composition observed. Instead, we observed a strong coloration change in the mats in response to shading, which could be due to positive phototaxis of Oscillatoria trichomes in the shaded mats. These results help inform how the prokaryotic communities in these highly productive mats may respond to future climate scenarios.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13348247/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148316424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The mobile resistome in the water-soil-air nexus: horizontal gene transfer and environmental dissemination of antimicrobial resistance genes. 水-土壤-空气关系中的移动抗性组：抗菌素抗性基因的水平转移和环境传播。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-06-18 DOI: 10.1093/femsec/fiag064

Christian Joseph N Ong, Rahmatullah Nazari, Kevin Smith P Cabuhat, Jerico Bautista Ogaya, Mohamed Mustaf Ahmed, Deborah Oluwaseun Shomuyiwa, Shuaibu Saidu Musa, Oshibe Joseph Daberechi, Yusuf Hared Abdi, Rich Milton R Dulay, Don Eliseo Lucero-Prisno

{"title":"The mobile resistome in the water-soil-air nexus: horizontal gene transfer and environmental dissemination of antimicrobial resistance genes.","authors":"Christian Joseph N Ong, Rahmatullah Nazari, Kevin Smith P Cabuhat, Jerico Bautista Ogaya, Mohamed Mustaf Ahmed, Deborah Oluwaseun Shomuyiwa, Shuaibu Saidu Musa, Oshibe Joseph Daberechi, Yusuf Hared Abdi, Rich Milton R Dulay, Don Eliseo Lucero-Prisno","doi":"10.1093/femsec/fiag064","DOIUrl":"10.1093/femsec/fiag064","url":null,"abstract":"The rapid emergence and global dissemination of antimicrobial resistance pose a serious threat to public health, environmental sustainability, and economic development. Central to this crisis is the resistome, defined as the collection of all antimicrobial resistance genes (ARGs) present in pathogenic and non-pathogenic micro-organisms across clinical, agricultural, and natural ecosystems. The environmental resistome plays a crucial role in the evolution and transmission of resistance, serving as both a reservoir and a conduit for ARG exchange through horizontal gene transfer. This review provides a comprehensive overview of the structure, diversity, and dynamics of the resistome, with emphasis on the interconnected water-soil-air continuum. Key mechanisms driving resistome dissemination, including mobile genetic elements such as plasmids, integrons, transposons, and bacteriophages, are discussed alongside the major routes of gene transfer, conjugation, transformation, and transduction. The review highlights anthropogenic drivers that intensify resistome expansion, including antibiotic misuse, wastewater discharge, agricultural runoff, and exposure to heavy metals, pesticides, and disinfectants, which promote co-selection. Advances in resistome profiling approaches, such as quantitative PCR, metagenomics, long-read sequencing, and functional metagenomics, are critically evaluated for their capacity to resolve ARG diversity, mobility, and host associations.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13322033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148270965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Linking composition and function: a two-year metatranscriptomic study of microbial adaptation in an industrial wastewater treatment plant. 连接组成和功能：一项为期两年的工业废水处理厂微生物适应的超转录组学研究。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-06-18 DOI: 10.1093/femsec/fiag051

Asala Mahajna, Ranko Gacesa, Karel J Keesman, Gert-Jan W Euverink, Andreas Froemelt, Carlos J Melián, Bayu Jayawardhana

{"title":"Linking composition and function: a two-year metatranscriptomic study of microbial adaptation in an industrial wastewater treatment plant.","authors":"Asala Mahajna, Ranko Gacesa, Karel J Keesman, Gert-Jan W Euverink, Andreas Froemelt, Carlos J Melián, Bayu Jayawardhana","doi":"10.1093/femsec/fiag051","DOIUrl":"10.1093/femsec/fiag051","url":null,"abstract":"Industrial saline wastewater presents a major challenge due to high salinity. While most previous studies focus on domestic activated sludge processes using 16S rRNA sequencing, this study provides metatranscriptomic insight into an industrial saline wastewater treatment plant in the Netherlands operating a facultative activated sludge process. The process, characterized by alternating aeration and non-aeration phases, generates dynamic redox conditions that drive microbial succession and adaptive metabolic responses over time, in contrast to conventional activated sludge processes that typically operate under more stable aeration regimes and comparatively steady redox conditions. Over two years and four months, 32 metatranscriptomic profiles were generated alongside comprehensive physicochemical and operational measurements. The activated sludge harbored a diverse, metabolically active community contributing to nitrogen, carbon, and phosphorus removal, as annotated via SEED Subsystems. Functional gene richness saturated more rapidly than taxonomic richness, reflecting substantial functional redundancy, while complementarity effects under lower-diversity conditions suggested cooperative interactions that enhance ecosystem functionality. Notably, Thermodesulfobacteriota, including sulfur-reducing Desulfobulbia, emerged as a core and environmentally filtered group under saline conditions. This study demonstrates that longitudinal metatranscriptomic profiling can capture temporally resolved functional responses in industrial microbial communities, offering insight into microbial resilience, adaptation, and the ecological principles underpinning engineered bioremediation systems.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13281742/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147962678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Giant viruses of the polar regions: diversity, endemism, adaptation and ecological structuring. 极地巨型病毒：多样性、地方性、适应性和生态结构。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-06-18 DOI: 10.1093/femsec/fiag061

Thomas M Pitot, Catherine Girard

{"title":"Giant viruses of the polar regions: diversity, endemism, adaptation and ecological structuring.","authors":"Thomas M Pitot, Catherine Girard","doi":"10.1093/femsec/fiag061","DOIUrl":"10.1093/femsec/fiag061","url":null,"abstract":"The poles represent Earth's most climate-sensitive biomes, where microbial communities and viruses drive fundamental ecological processes. Within these extreme environments, giant viruses of the phylum Nucleocytoviricota have emerged as key regulators of microbial mortality and biogeochemical cycling. This review synthesizes current knowledge on polar giant viruses, emphasizing their diversity, endemism, genomic adaptations, and ecological roles across polar habitats. Polar systems harbour highly structured, habitat-specific viral assemblages characterized by significant endemism and sharp ecological boundaries, shaped by strong environmental filtering, host biogeography, virus-virus interactions and spatial isolation. Genomic analyses show that these viruses possess unique adaptations to persistent cold, including proteomic shifts consistent with psychrophily and the enrichment of auxiliary metabolic genes. Interactions with giant virus parasites (virophages) further contribute to the complexity of polar giant virus ecology. However, rapid warming and the loss of perennial ice threaten to destabilize these ancient refugia and their giant virus populations. Changes in temperature, hydrological connectivity and ecosystem structure may alter virus-host dynamics and weaken the strong viral endemism. These environmental shifts risk the extinction of unique lineages and the disruption of the critical biogeochemical roles they perform, highlighting the urgent need to understand viral dynamics in rapidly changing polar and cryospheric ecosystems.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13335480/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148204665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The plastisphere: not a unique biofilm but a unifying concept for the interdisciplinary plastic biofilm research community. 塑料球：不是一个独特的生物膜，而是跨学科塑料生物膜研究界的统一概念。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-06-18 DOI: 10.1093/femsec/fiag055

Priscilla Carrillo-Barragán, Elisenda Ballesté, Michael Sauer, Joseph Christie-Oleza

{"title":"The plastisphere: not a unique biofilm but a unifying concept for the interdisciplinary plastic biofilm research community.","authors":"Priscilla Carrillo-Barragán, Elisenda Ballesté, Michael Sauer, Joseph Christie-Oleza","doi":"10.1093/femsec/fiag055","DOIUrl":"10.1093/femsec/fiag055","url":null,"abstract":"Plastic has introduced a novel and persistent substrate into natural ecosystems, rapidly colonized by microbial biofilms collectively termed the plastisphere. Since its introduction, the concept has catalyzed interdisciplinary research and shaped scientific and public discourse on plastic pollution. Yet, a central question remains unresolved: Do plastisphere communities represent a fundamentally distinct ecological entity, or are they conventional biofilms forming on an unconventional material? Here, we synthesize current evidence across marine and terrestrial systems to argue that plastisphere communities are not consistently taxonomically or functionally unique. Instead, they largely reflect established biofilm assembly processes governed by environmental conditions, source communities, and successional dynamics. Claims of plastic biodegradation, pathogen enrichment, or antimicrobial resistance hotspots remain context-dependent and often lack robust comparative frameworks. We propose that the ecological significance of the plastisphere lies not in microbial novelty, but in the properties of the substrate itself. Plastics are uniquely persistent and, in many environments, highly mobile, enabling microbial communities to disperse across ecosystems and extend residence times beyond those of natural particles. By reframing the plastisphere as a condition of microbial life on durable, mobile substrates, we retain its conceptual value while aligning it with ecological theory and advancing a more precise research agenda.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13289607/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148301529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The respiratory microbiome: dynamics from health to disease. 呼吸微生物组：从健康到疾病的动态。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-06-18 DOI: 10.1093/femsec/fiag058

Wenxin Lin, Zheng Sun, Jingxian Chen, Shenghai Huang

{"title":"The respiratory microbiome: dynamics from health to disease.","authors":"Wenxin Lin, Zheng Sun, Jingxian Chen, Shenghai Huang","doi":"10.1093/femsec/fiag058","DOIUrl":"10.1093/femsec/fiag058","url":null,"abstract":"Research on the respiratory microbiome has moved beyond the sterile-lung paradigm, but disease-associated microbial patterns are still often described as static signatures. In this mini-review, we synthesize current evidence within a dynamic state-transition framework in which respiratory microbial communities are shaped by microbial immigration, elimination, local growth conditions, and host inflammatory tone. This framework traces the respiratory microbiome from early-life assembly and homeostatic maintenance to perturbation, recovery, or persistence in alternative ecological states. We discuss how barrier integrity, mucociliary clearance, mucus and nutrient landscapes, inflammatory feedback, microbial metabolites, and the gut-lung axis regulate microbial stability and disease susceptibility. Across asthma, chronic obstructive pulmonary disease, cystic fibrosis, bronchiectasis, and respiratory infection, dysbiosis is interpreted not as a set of disease-specific taxa, but as a context-dependent outcome of shared ecological mechanisms. We also highlight methodological and translational priorities, including contamination control in low-biomass samples, longitudinal sampling, multi-omics integration, spatial host profiling, and cautious interpretation of association versus causality. Viewing the respiratory microbiome as an ecological system in motion may better connect microbial dynamics with disease heterogeneity, risk stratification, and future microbiome-directed interventions.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13308348/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148301586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Impacts of conventional and organic farming practices on soil and aquatic microbial communities in rice (Oryza sativa) agricultural fields in Southern Brazil. 传统和有机耕作方式对巴西南部水稻农田土壤和水生微生物群落的影响

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-06-18 DOI: 10.1093/femsec/fiag059

Fernanda B Gazulha, Carla S R Huber, Luciano K Huber, Gabriel Rubensam, Valentina Brocker-Junqueira, Eduardo Moreira da Silva, Joe D Taylor, Laura R P Utz

{"title":"Impacts of conventional and organic farming practices on soil and aquatic microbial communities in rice (Oryza sativa) agricultural fields in Southern Brazil.","authors":"Fernanda B Gazulha, Carla S R Huber, Luciano K Huber, Gabriel Rubensam, Valentina Brocker-Junqueira, Eduardo Moreira da Silva, Joe D Taylor, Laura R P Utz","doi":"10.1093/femsec/fiag059","DOIUrl":"10.1093/femsec/fiag059","url":null,"abstract":"Microbial communities play essential roles in agroecosystem functioning, yet the effects of different rice farming practices on their structure and dynamics remain underexplored, particularly across soil and water compartments. This study compared microbial assemblages in organic and conventional rice fields in southern Brazil over a single growing season, based on ten samples collected from two fields. High-throughput sequencing of 16S region V3V4 and 18S region V4 rRNA genes was used to profile bacteria, unicellular eukaryotes, fungi, and metazoa at three time points during rice cultivation. Community composition and diversity differed between farming systems and over time. In soil, bacterial richness was higher in conventional systems at specific time points but showed greater temporal variability. In water, microbial communities in organic systems were generally more diverse and stable, with significantly lower bacterial richness in conventional systems at the initial sampling point (P < 0.01). Unicellular eukaryotes and metazoa showed strong farming-system responses, particularly in water, where organic fields supported more diverse assemblages. These findings highlight the influence of farming practices on microbial biodiversity and emphasize the importance of integrated, multi-group approaches for understanding agroecosystem functioning.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13285872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148175762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bacterial and microeukaryotic assemblage transitions during a harmful algal bloom in the Nakdong River. 洛东江有害藻华期间细菌和微真核生物组合的转变。

IF 4.1 3区生物学

FEMS microbiology ecology Pub Date : 2026-06-18 DOI: 10.1093/femsec/fiag057

Dayun Kang, Min-Ji Kim, Seungjun Lee

{"title":"Bacterial and microeukaryotic assemblage transitions during a harmful algal bloom in the Nakdong River.","authors":"Dayun Kang, Min-Ji Kim, Seungjun Lee","doi":"10.1093/femsec/fiag057","DOIUrl":"10.1093/femsec/fiag057","url":null,"abstract":"Harmful algal blooms (HABs) represent major ecological disturbances that can alter microbial community composition and reduce ecosystem resilience. Here, we investigated bacterial and microeukaryotic assemblage transitions during a bloom-affected period in the Nakdong River, a regulated river system in South Korea. By integrating microcystin (MC) measurements, cyanobacterial dominance, water-quality parameters, and amplicon-based community profiling (16S rRNA gene and ITS2), we characterized how microbial communities reorganized along gradients of bloom intensity. MC concentrations increased markedly across the sampling period, and early-phase qPCR data showed concurrent increases in mcyE gene abundance through 6 August 2021. Bacterial communities shifted from Actinobacteriota- and Proteobacteria-dominated assemblages toward Microcystaceae-enriched communities. Microeukaryotic communities similarly transitioned from diverse Chlorophyta, fungi, and ciliates to Chlamydomonadaceae- and ciliate-dominated assemblages under high-MC conditions. Both domains exhibited significant reductions in alpha diversity with increasing bloom intensity, although microeukaryotic responses were comparatively moderate. Correlation analyses revealed strong associations of MC concentration and Microcystis abundance with declining pH, elevated BOD, and the enrichment of bloom-associated taxa. These results indicate that bloom-associated conditions in this regulated river system were accompanied by parallel restructuring of bacterial and microeukaryotic assemblages. The integration of environmental and microbial indicators presented here provides a framework for understanding HAB-associated microbial reorganization and for informing monitoring strategies in hydrologically altered freshwater ecosystems.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2026-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13278487/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148143248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0